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- PDB-2rch: Crystal Structure of Arabidopsis thaliana Allene Oxide Synthase (... -

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Basic information

Entry
Database: PDB / ID: 2rch
TitleCrystal Structure of Arabidopsis thaliana Allene Oxide Synthase (AOS, cytochrome P450 74A, CYP74A) Complexed with 13(S)-HOD at 1.85 A Resolution
ComponentsCytochrome P450 74A
KeywordsLYASE / P450 fold / Chloroplast / Fatty acid biosynthesis / Heme / Iron / Lipid synthesis / Metal-binding / Oxylipin biosynthesis / Transit peptide
Function / homology
Function and homology information


oxylipin metabolic process / hydroperoxide dehydratase / allene oxide synthase activity / jasmonic acid biosynthetic process / response to jasmonic acid / plastoglobule / chloroplast thylakoid / epoxygenase P450 pathway / oxylipin biosynthetic process / response to fungus ...oxylipin metabolic process / hydroperoxide dehydratase / allene oxide synthase activity / jasmonic acid biosynthetic process / response to jasmonic acid / plastoglobule / chloroplast thylakoid / epoxygenase P450 pathway / oxylipin biosynthetic process / response to fungus / chloroplast envelope / thylakoid / plastid / chloroplast thylakoid membrane / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / defense response to fungus / chloroplast / monooxygenase activity / oxygen binding / defense response / response to wounding / iron ion binding / heme binding / mitochondrion
Similarity search - Function
Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(9Z,11E,13S)-13-hydroxyoctadeca-9,11-dienoic acid / PROTOPORPHYRIN IX CONTAINING FE / Allene oxide synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsLee, D.S. / Nioche, P. / Raman, C.S.
CitationJournal: Nature / Year: 2008
Title: Structural insights into the evolutionary paths of oxylipin biosynthetic enzymes.
Authors: Lee, D.S. / Nioche, P. / Hamberg, M. / Raman, C.S.
History
DepositionSep 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 8, 2014Group: Source and taxonomy
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 74A
B: Cytochrome P450 74A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,1556
Polymers111,5332
Non-polymers1,6224
Water12,376687
1
A: Cytochrome P450 74A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6803
Polymers55,7671
Non-polymers9132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 74A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4753
Polymers55,7671
Non-polymers7092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.552, 105.336, 162.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome P450 74A / Allene oxide synthase / Hydroperoxide dehydrase


Mass: 55766.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYP74A, AOS / Plasmid: pcWori+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q96242, hydroperoxide dehydratase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-243 / (9Z,11E,13S)-13-hydroxyoctadeca-9,11-dienoic acid


Mass: 296.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H32O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG4000, Glycerol, Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 5, 2007
RadiationMonochromator: double miror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. all: 93014 / Num. obs: 93014 / % possible obs: 99.1 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.85→1.9 Å / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-IceIcedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2PHQ

2phq
PDB Unreleased entry


Resolution: 1.85→88.39 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.532 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20477 4657 5 %RANDOM
Rwork0.17097 ---
all0.17262 88280 --
obs0.17262 88280 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.364 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.85→88.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7418 0 113 687 8218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227855
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3572.01110666
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8715956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.423.446354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66151336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7151554
X-RAY DIFFRACTIONr_chiral_restr0.0930.21131
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026020
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.23585
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25434
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2609
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8651.54855
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33427641
X-RAY DIFFRACTIONr_scbond_it2.35933400
X-RAY DIFFRACTIONr_scangle_it3.6134.53021
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 349 -
Rwork0.217 6344 -
obs--97.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.553-0.03570.16770.5864-0.02120.53790.0056-0.0116-0.05270.0417-0.01250.03760.05730.03090.0069-0.04070.00680.0163-0.05540.007-0.06782.425731.278432.0427
20.6822-0.1967-0.09090.58350.12460.71620.02110.03070.01930.0176-0.0154-0.0497-0.0105-0.0489-0.0057-0.0465-0.0059-0.0022-0.04350.009-0.085223.899659.95443.2939
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA52 - 48625 - 459
2X-RAY DIFFRACTION2BB52 - 48625 - 459

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